Identification of pore spaces in 3D CT soil images using a PFCM partitional clustering

Recent advances in non-destructive imaging techniques, such as X-ray computed tomography (CT), make it possible to analyse pore space features from the direct visualisation from soil structures. A quantitative characterisation of the three-dimensional solid-pore architecture is important to understand soil mechanics, as they relate to the control of biological, chemical, and physical processes across scales. This analysis technique therefore offers an opportunity to better interpret soil strata, as new and relevant information can be obtained. In this work, we propose an approach to automatically identify the pore structure of a set of 200-2D images that represent slices of an original 3D CT image of a soil sample, which can be accomplished through non-linear enhancement of the pixel grey levels and an image segmentation based on a PFCM (Possibilistic Fuzzy C-Means) algorithm. Once the solids and pore spaces have been identified, the set of 200-2D images is then used to reconstruct an approximation of the soil sample by projecting only the pore spaces. This reconstruction shows the structure of the soil and its pores, which become more bounded, less bounded, or unbounded with changes in depth. If the soil sample image quality is sufficiently favourable in terms of contrast, noise and sharpness, the pore identification is less complicated, and the PFCM clustering algorithm can be used without additional processing; otherwise, images require pre-processing before using this algorithm. Promising results were obtained with four soil samples, the first of which was used to show the algorithm validity and the additional three were used to demonstrate the robustness of our proposal. The methodology we present here can better detect the solid soil and pore spaces on CT images, enabling the generation of better 2D?3D representations of pore structures from segmented 2D images.

Composition of pore water and diagenetic carbonates of ODP Site 123-765

Degradation of organic matter in slightly organic-rich (1 wt% organic carbon) Neogene calcareous turbidites of the Argo Basin at Site 765 by sulfate reduction results in pore-water phosphate, ammonium, manganese, and carbonate alkalinity maxima. Pore-water calcium and magnesium decrease in the uppermost 100 meters below seafloor (mbsf) in response to the precipitation of calcian dolomite with an average composition of Ca1.15Mg0.83Fe0.02(CO3)2. Clear, euhedral dolomite rhombs range from <1 to 40 µm in diameter and occur in trace to minor amounts (<1-2 wt%) in Pleistocene to Pliocene sediment (62-210 mbsf) The abundance of dolomite increases markedly (2-10 wt%) in Miocene sediment (210-440 mbsf). The dolomite is associated with diagenetic sepiolite and palygorskite, as well as redeposited biogenic low-Mg calcite and aragonitic benthic foraminifers. Currently, dolomite is precipitating at depth within the pore spaces of the sediment, largely as a result of aragonite dissolution. The rate of aragonite dissolution, calculated from the pore-water strontium profile, is sufficient to explain the amount of dolomite observed at Site 765. A foraminiferal aragonite precursor is further supported by the carbon and oxygen isotopic compositions of the dolomite, which are fairly close to the range of isotopic compositions observed for Miocene benthic foraminifers. Dolomite precipitation is promoted by the degradation of organic matter by sulfate-reducing bacteria because the lower pore-water sulfate concentration reduces the effect of sulfate inhibition on the dolomite reaction and because the higher carbonate alkalinity increases the degree of saturation of the pore waters with dolomite. Organic matter degradation also results in the precipitation of pyrite and trace amounts of apatite (francolite), and the release of iron and manganese to the pore water by reduction of Fe and Mn oxides. Spherical, silt-sized aggregates of microcrystalline calcian rhodochrosite occur in trace to minor amounts in Lower Cretaceous sediment from 740 to 900 mbsf at Site 765. A negative carbon isotopic composition suggests that the rhodochrosite formed early in the sulfate reduction zone, but a depleted oxygen isotopic composition suggests that the rhodochrosite may have recrystallized at deeper burial depths.

Image sub-segmentation by PFCM and Artificial Neural Networks to detect pore space in 2D and 3D CT soil images

The image by Computed Tomography is a non-invasive alternative for observing soil structures, mainly pore space. The pore space correspond in soil data to empty or free space in the sense that no material is present there but only fluids, the fluid transport depend of pore spaces in soil, for this reason is important identify the regions that correspond to pore zones. In this paper we present a methodology in order to detect pore space and solid soil based on the synergy of the image processing, pattern recognition and artificial intelligence. The mathematical morphology is an image processing technique used for the purpose of image enhancement. In order to find pixels groups with a similar gray level intensity, or more or less homogeneous groups, a novel image sub-segmentation based on a Possibilistic Fuzzy c-Means (PFCM) clustering algorithm was used. The Artificial Neural Networks (ANNs) are very efficient for demanding large scale and generic pattern recognition applications for this reason finally a classifier based on artificial neural network is applied in order to classify soil images in two classes, pore space and solid soil respectively.

Relations between coal petrology and gas content in the Upper Newlands Seam, central Queensland, Australia

The Upper Newlands Seam in the northern Bowen Basin, Queensland, Australia consists of six benches (A-F) that have different petrographic assemblages. Benches C and E contain relatively abundant inertodetrinite and mineral matter, as well as anomalously high reflectance values; these characteristics support a largely allochthonous, detrital origin for the C and E benches. Fractures and cleats in the seam show a consistent orientation of northeast- southwest for face cleats, and a wide range of orientations for fractures. Cleat systems are well developed in bright bands, with poor continuity in the dull coal. Both maceral content and cleat character are suggested to influence gas drainage in the Upper Newlands Seam. A pronounced positive correlation between vitrinite abundance and gas desorption data suggests more efficient drainage from benches with abundant vitrinite. Conversely, inertinite-rich benches are suggested to have less efficient drainage, and possibly retain gas within pore spaces, which could increase the outburst potential of the coal. (C) 2001 Elsevier Science BN. All rights reserved.

Iron oxidation on the surface of adventitious roots and its relation to aerenchyma formation in rice genotypes

Establishment of the water layer in an irrigated rice crop leads to consumption of free oxygen in the soil which enters in a chemical reduction process mediated by anaerobic microorganisms, changing the crop environment. To maintain optimal growth in an environment without O2, rice plants develop pore spaces (aerenchyma) that allow O2 transport from air to the roots. Carrying capacity is determined by the rice genome and it may vary among cultivars. Plants that have higher capacity for formation of aerenchyma should theoretically carry more O2 to the roots. However, part of the O2 that reaches the roots is lost due to permeability of the roots and the O2 gradient created between the soil and roots. The O2 that is lost to the outside medium can react with chemically reduced elements present in the soil; one of them is iron, which reacts with oxygen and forms an iron plaque on the outer root surface. Therefore, evaluation of the iron plaque and of the formation of pore spaces on the root can serve as a parameter to differentiate rice cultivars in regard to the volume of O2 transported via aerenchyma. An experiment was thus carried out in a greenhouse with the aim of comparing aerenchyma and iron plaque formation in 13 rice cultivars grown in flooded soils to their formation under growing conditions similar to a normal field, without free oxygen. The results indicated significant differences in the volume of pore spaces in the roots among cultivars and along the root segment in each cultivar, indicating that under flooded conditions the genetic potential of the plant is crucial in induction of cell death and formation of aerenchyma in response to lack of O2. In addition, the amount of Fe accumulated on the root surface was different among genotypes and along the roots. Thus, we concluded that the rice genotypes exhibit different responses for aerenchyma formation, oxygen release by the roots and iron plaque formation, and that there is a direct relationship between porosity and the amount of iron oxidized on the root surface.

Studies on the taxonomy of interstitial Fauna of some prominent beaches of Kerala

The oceans in their expanse cover, seven - tenths of the Earth surface. Despite being restricted in size, the littoral zone or the intertidal zone (beach) has the greatest variation in environment factors of any marine area .Stemming from this variation ,a treamendous diversity of life, which may be great as or greater than that found in the more extensive sub tidal habits exist in this realm. the study beaches harbour diverse and abundant assemblage of marine organisms. Besides macro funna, microscopic organisms belonging to the lower and higher invertebrate taxa profusely inhabit these beaches. The ecological realm where these animals exist is known as the interstitial environment, which in principle includes the pore spaces in between the sand grains containing copious supply of nutrient rich oxygenated seawater. An astonishing diversity of taxa could be found within the interstitial fauna.

Modelo fractal para resistividade complexa de rochas: interpretação petrofísica e aplicação à exploração geoelétrica

Rochas contendo metálicos disseminados ou partículas de argila em ambiente natural onde soluções eletrolíticas normalmente preenchem os poros das rochas, exibem um tipo de polarização em baixas freqüências conhecido como polarização induzida. Nesta tese foi desenvolvido um novo modelo para descrever o fenômeno de polarização das rochas, não apenas em baixas freqüências, mas compreendendo todo o espectro eletromagnético, possível de utilização na prospecção geoelétrica. Este novo modelo engloba a maioria dos modelos utilizados até o momento como casos especiais, além de superar as limitações dos mesmos. Seu circuito analógico inclui uma impedância não linear do tipo r (iwtf)^-n que simula o efeito das superfícies rugosas das interfaces entre os grãos bloqueadores (partículas metálicas e/ou de argilas) e o eletrólito. A impedância de Warburg generalizada está em série com a resistência dos grãos bloqueadores da passagem de corrente e em paralelo com a impedância da dupla camada associada a essas interfaces. Esta combinação está em série com a resistência do eletrólito nas passagens dos poros bloqueados. Os canais não bloqueados são representados por uma resistência que corresponde à resistividade normal CC da rocha. A combinação desta resistência com a capacitância "global" da rocha é finalmente conectada em paralelo ao resto do circuito mencionado acima. Os parâmetros deste modelo incluem a resistividade CC (p₀), a cargueabilidade (m), três tempos de relaxação (t, Tf and T2), um fator de resistividade de grãos (δ_r), e o expoente de freqüência (η). O tempo de relaxação fractal (Tf), e o expoente de frequencia (η) estão relacionados à geometria fractal das interfaces rugosas entre os minerais condutivos (grãos metálicos e/ou partículas de argila bloqueando os canais dos poros) e o eletrólito. O tempo de relaxação (T) é um resultado da relaxação em baixa freqüência das duplas camadas elétricas formadas nas interfaces eletrólito-cristais, enquanto (T₀) é o tempo de relaxação macroscópico da amostra como um todo. O fator de resistividade dos grãos (δ_r) relaciona a resistividade dos grãos condutivos com o valor de resistividade CC da rocha. A resistividade CC da rocha (p₀), e δ_r estão relacionados à porosidade, à condutividade do eletrólito e às relações mineralógicas entre a matriz e os grãos condutivos. O modelo foi testado sobre um intervalo largo de freqüências contra dados experimentais de amplitude e fase da resistividade bem como para dados de constante dielétrica complexa. Os dados utilizados neste trabalho foram obtidos a partir da digitalização de dados experimentais publicados, obtidos por diversos autores e englobando amostras de rochas sedimentares, ígneas e metam6rficas. É mostrado neste trabalho que os parâmetros deste modelo permitem identificar diferenças texturais e mineralógicas nas rochas. Bote modelo foi introduzido, primeiramente, como propriedade intrínseca de um semiespaço homogêneo sendo demonstrado, neste trabalho, que a resposta observada em superfície reflete as propriedades intrínsecas do meio polarizável, sendo o acoplamento eletromagnético desprezível em freqüências menores que 104 Hz. Em seguida, o meio polarizável foi embebido em um pacote de N camadas sendo demonstrado que os parâmetros fractais do meio polarizável podem ser obtidos do levantamento em superfície para diferentes espessuras dessa camada. Isto justifica a utilização pura e simples de modelos de polarização desenvolvidos para amostras em laboratório para ajustar dados de campo, o que vem sendo feito sem uma justificativa bem fundamentada. Estes resultados demonstram a importância para a prospecção geolétrica do modelo proposto nesta tese.

Modellierung von Porenraumgeometrien und Transport in korngestützten porösen Medien

Poröse Medien spielen in der Hydrosphäre eine wesentliche Rolle bei der Strömung und beim Transport von Stoffen. In diesem Raum finden komplexe Prozesse statt: Advektion, Kon-vektion, Diffusion, hydromechanische Dispersion, Sorption, Komplexierung, Ionenaustausch und Abbau. Die strömungsmechanischen- und die Transportverhältnisse in porösen Medien werden direkt durch die Geometrie des Porenraumes selbst und durch die Eigenschaften der transportierten (oder strömenden) Medien bestimmt. In der Praxis wird eine Vielzahl von empirischen Modellen verwendet, die die Eigenschaften des porösen Mediums in repräsentativen Elementarvolumen wiedergeben. Die Ermittlung der in empirischen Modellen verwendeten Materialparameter erfolgt über Labor- oder Feldbestimmungsmethoden. Im Rahmen dieser Arbeit wurde das Computer-modell PoreFlow entwickelt, welches die hydraulischen Eigenschaften eines korngestützten porösen Mediums aus der mikroskopischen Modellierung des Fluidflusses und Transportes ableitet. Das poröse Modellmedium wird durch ein dreidimensionales Kugelpackungsmodell, zusam-mengesetzt aus einer beliebigen Kornverteilung, dargestellt. Im Modellporenraum wird die Strömung eines Fluids basierend auf einer stationären Lösung der Navier-Stokes-Gleichung simuliert. Die Ergebnisse der Modellsimulationen an verschiedenen Modellmedien werden mit den Ergebnissen von Säulenversuchen verglichen. Es zeigt sich eine deutliche Abhängigkeit der Strömungs- und Transportparameter von der Porenraumgeometrie sowohl in den Modell-simulationen als auch in den Säulenexperimenten.

Lithofacies, chronostratigraphy, minerals and diagenetic silica facies at DSDP Leg 80 Holes

X-ray powder diffraction and optical and scanning-electron microscope analyses of sediment samples taken from four sites drilled in the Goban Spur area of the northeast Atlantic show variable diagenetic silicification of sediments at several stratigraphic horizons. The results are as follows: 1. The silicified sediments are middle Eocene at Site 548, Paleocene to lower Albian at Site 549, upper to lower Paleocene at Site 550, and lower Turanian at Site 551. 2. There are three types of these silicified sediments: nodular type in carbonate-rich host sediments, bedded type in clayey host sediments, and a type transitional between the other two. 3. Silica diagenesis is considered to progress as follows: dissolution of siliceous fossils; precipitation of opal CT in pore spaces and transformation of biogenic silica (opal A) to opal CT, development of opal CT cement; chalcedonic quartz precipitation in pore spaces and replacement of foraminiferal tests by chalcedonic quartz; and finally, transformation of opal CT to quartz, and cementation. But the strong influence of host-sediment types on diagenetic silica fades is recognized. Bedded-type silicified sediments in a clayey environment indicate a lower grade of silica diagenesis. Only very weak chalcedonic quartz formation is recognized, and there is no opal CT cementation, even in Lower Cretaceous bedded-type clayey silicified sediments. 4. The rf(101) spacing of opal CT shows two distinct trends of ordering or decrease with burial depth; one is a rapid change, in the case of nodular silicified sediments, and the other is a more gentle shift, found in bedded silicified sediments. 5. Diagenetic silica facies of the nodular type develop as irregular concentric zones around some nodule nuclei. Also, quartz-chert nodule formation occurs at rather shallower horizons, and is discordant with the trend of decreasing d(101) spacing in opal CT. 6. Silicified sediments at Site 551 are shallower than at the other sites. The diagenetic silica facies suggest the probable erosion of 300 m or more of sediment at this site. 7. The zeolites clinoptilolite and phillipsite were found in the sediment samples recovered on Leg 80. Clinoptilolite occurs from the shallower levels to the deepest horizons of diagenetically silicified zones, suggesting that clinoptilolite formation is related to diagenesis of biogenic silica. Phillipsite at Site 551 (Section 551-5-2) may originate from volcanogenie material.

Diagenesis of siliceous particles in ODP Hole 114-699A

A number of neogenic opaline structures, not previously reported in the literature, as well as other neogenic phases are described from four Oligocene to Pliocene biosiliceous sediment samples from Hole 699A. The possible influence of microbes on the formation or the morphology of some of them is discussed. The samples, which are early Pliocene, early to middle Miocene, and late Oligocene (two) in age, were histologically fixed aboard ship upon retrieval. Investigations of the samples used SEM (with Edax/Tracor) and XRD methods. Diagenesis has affected all four samples, but the most extensive development of neoformed structures occurs in the Miocene and uppermost Oligocene samples, where microbial filaments (0.05 to 10 ?m long), microbial colonies, and siliceous microhemispheroids (0.2 to 0.7 µm diameter) were observed. The latter encrust filaments, diatoms, and detrital grains to varying degrees. Other neoformed structures include (1) flakes formed by coalesced microhemispheroids, some of which are guided by short, stubby filaments, which occur only in the Miocene and uppermost Oligocene samples, and (2) flakes characterized by smooth or microfissured surfaces, which grow on diatom frustules and in pore spaces and have a more widespread distribution. The XRD data indicate possible cristobalite formation in the Miocene and uppermost Oligocene samples; we believe that the neoformed opaline structures (encrusted filaments and microhemispheroids) may represent an early phase of opal-CT. The timing of neoformation of most of these features appears to have been fairly recent, continuing even at the time of sampling. There appears to be no direct correlation of this incipient, lower Miocene-uppermost Oligocene diagenetic layer and the pore-water chemistry profiles; a massive increase in shear strength in these sediments, however, may indicate some cementation. Smectite was identified by XRD as the most prominent clay mineral in these generally clay-poor sediments. Honeycombed minerals with filamentous edges, which could correspond to smectite, were observed with SEM in the pore spaces.

Three-dimensional tracking of motile bacteria near a solid planar surface.

Knowing how motile bacteria move near and along a solid surface is crucial to understanding such diverse phenomena as the migration of infectious bacteria along a catheter, biofilm growth, and the movement of bacteria through the pore spaces of saturated soil, a critical step in the in situ bioremediation of contaminated aquifers. In this study, a tracking microscope is used to record the three-dimensional motion of Escherichia coli near a planar glass surface. Data from the tracking microscope are analyzed to quantify the effects of bacteria-surface interactions on the swimming behavior of bacteria. The speed of cells approaching the surface is found to decrease in agreement with the mathematical model of Ramia et al. [Ramia, M., Tullock, D. L. & Phan-Tien, N. (1993) Biophys J. 65,755-778], which represents the bacteria as spheres with a single polar flagellum rotating at a constant rate. The tendency of cells to swim adjacent to the surface is shown in computer-generated reproductions of cell traces. The attractive interaction potential between the cells and the solid surface is offered as one of several possible explanations for this tendency.

Assessment of physical and hydrological properties of biological soil crusts using x-ray microtomography and modelling

Biological soil crusts (BSCs) are formed by aggregates of soil particles and communities of microbial organisms and are common in all drylands. The role of BSCs on infiltration remains uncertain due to the lack of data on their role in affecting soil physical properties such as porosity and structure. Quantitative assessment of these properties is primarily hindered by the fragile nature of the crusts. Here we show how the use of a combination of non-destructive imaging X-ray microtomography (XMT) and Lattice Boltzmann method (LBM) enables quantification of key soil physical parameters and the modeling of water flow through BSCs samples from Kalahari Sands, Botswana. We quantify porosity and flow changes as a result of mechanical disturbance of such a fragile cyanobacteria-dominated crust. Results show significant variations in porosity between different types of crusts and how they affect the flow and that disturbance of a cyanobacteria-dominated crust results in the breakdown of larger pore spaces and reduces flow rates through the surface layer. We conclude that the XMT–LBM approach is well suited for study of fragile surface crust samples where physical and hydraulic properties cannot be easily quantified using conventional methods.

Wall mediated transport in confined spaces: Exact theory for low density

We present a theory for the transport of molecules adsorbed in slit and cylindrical nanopores at low density, considering the axial momentum gain of molecules oscillating between diffuse wall reflections. Good agreement with molecular dynamics simulations is obtained over a wide range of pore sizes, including the regime of single-file diffusion where fluid-fluid interactions are shown to have a negligible effect on the collective transport coefficient. We show that dispersive fluid-wall interactions considerably attenuate transport compared to classical hard sphere theory.

Influence of adsorbate interaction on transport in confined spaces

This article provides a review of the recent theory of transport in nanopores developed in the author's laboratory. In particular the influence of fluid-solid interactions on the transport coefficient is examined, showing that such interactions reduce the value of the coefficient by almost an order of magnitude in comparison to the Knudsen theory for non-interacting systems. The activation energy and potential energy barriers for diffusion in smooth pores with a one-dimensional potential energy profile are also discussed, indicating the inadequacy of the commonly used assumption of proportionality between the activation energy and heat of adsorption or the minimum pore potential energy. A further feature affected by fluid-solid interactions is the nature of the reflection of fluid molecules colliding with a pore wall surface, varying from being nearly specular - such as in carbon nanotubes - to nearly diffuse for amorphous solids. Diffuse reflection leads to momentum loss and reduced transport coefficients. However, fluid-solid interactions do not affect the transport coefficient in the single-file diffusion regime when the surface reflection is diffuse, and the transport coefficient in this case is largely independent of the adsorbed density.

Comparative Study of the Changes in Partial Pressure of Plasma Carbon Dioxide During Carbon Dioxide Insufflation into the Intraperitoneal and Preperitoneal Spaces

Background: We aimed to compare plasma concentrations of carbon dioxide (CO(2)) in dogs that underwent intra- and preperitoneal CO(2) insufflation. Materials and Methods: Thirty dogs were studied. Ten formed a control group, 10 underwent intraperitoneal CO(2) insufflation, and 10 underwent preperitoneal CO(2) insufflation. General anesthesia with controlled ventilation was standardized for all dogs. After stabilizing the anesthesia, blood samples were collected at predetermined times and were sent for immediate gasometric analysis. Analysis of variance was used for comparing variables. Results: The plasma CO(2) concentration in the intraperitoneal insufflation group increased significantly more than in the preperitoneal insufflation group and was significantly greater than in the control group (P < 0.05). The pH values in the intraperitoneal group were lower than in the preperitoneal group (P < 0.05). Conclusion: The data from this study suggest that a greater plasma concentration of CO(2) is achieved by insufflation at constant pressure into the intraperitoneal space than into the preperitoneal space.